Each day, about 74 people are recipients of organ transplants. Depending on the transplanted organ, many, if not all patients experience an episode of immunorejection. Biopsy of the transplanted organ is one method to confirm rejection; however this invasive approach makes it suboptimal for many patients for a variety of reasons, including patient discomfort, inconvenience, low but definite risks of morbidity and death, and increased health care costs. Biopsy procedures often suffer from sampling errors and variable, subjective pathological interpretation. In addition, there is emerging evidence that a transplanted organ may show a ‘clinical rejection’ despite a ‘normal’ pathologic specimen, suggesting a dysregulation that occurs at the molecular level preceding the onset of cellular rejection. Thus, non-invasive monitoring of transplant rejection would provide a less costly, and more convenient method of monitoring transplant rejection in patients. Further, non-invasive monitoring of transplant rejection would provide an earlier means for detecting transplant rejection. However, no alternative to the invasive biopsy procedure currently exists. Accordingly, improved methods and compositions for the non-invasive detection of organ rejection are needed.